[{"author":[{"last_name":"Gabrielaitis","id":"4D5B0CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Mantas","orcid":"0000-0002-7758-2016","full_name":"Gabrielaitis, Mantas"}],"article_type":"original","date_updated":"2023-08-10T14:19:33Z","acknowledgement":"The author thanks his colleagues K. Huszár and G. Tkačik for valuable discussions and comments on the manuscript.","volume":69,"date_created":"2021-08-08T22:01:31Z","_id":"9828","external_id":{"arxiv":["2102.04832"],"isi":["000682123900002"]},"citation":{"chicago":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” <i>IEEE Transactions on Signal Processing</i>. Institute of Electrical and Electronics Engineers, 2021. <a href=\"https://doi.org/10.1109/TSP.2021.3087899\">https://doi.org/10.1109/TSP.2021.3087899</a>.","ama":"Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals. <i>IEEE Transactions on Signal Processing</i>. 2021;69:4039-4054. doi:<a href=\"https://doi.org/10.1109/TSP.2021.3087899\">10.1109/TSP.2021.3087899</a>","ista":"Gabrielaitis M. 2021. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 69, 4039–4054.","mla":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” <i>IEEE Transactions on Signal Processing</i>, vol. 69, Institute of Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:<a href=\"https://doi.org/10.1109/TSP.2021.3087899\">10.1109/TSP.2021.3087899</a>.","apa":"Gabrielaitis, M. (2021). Fast and accurate amplitude demodulation of wideband signals. <i>IEEE Transactions on Signal Processing</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/TSP.2021.3087899\">https://doi.org/10.1109/TSP.2021.3087899</a>","short":"M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.","ieee":"M. Gabrielaitis, “Fast and accurate amplitude demodulation of wideband signals,” <i>IEEE Transactions on Signal Processing</i>, vol. 69. Institute of Electrical and Electronics Engineers, pp. 4039–4054, 2021."},"scopus_import":"1","intvolume":"        69","day":"09","arxiv":1,"isi":1,"department":[{"_id":"GaTk"}],"month":"06","quality_controlled":"1","publisher":"Institute of Electrical and Electronics Engineers","page":"4039 - 4054","year":"2021","publication_status":"published","publication_identifier":{"issn":["1053-587X"],"eissn":["1941-0476"]},"date_published":"2021-06-09T00:00:00Z","oa_version":"Preprint","status":"public","oa":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"abstract":[{"text":"Amplitude demodulation is a classical operation used in signal processing. For a long time, its effective applications in practice have been limited to narrowband signals. In this work, we generalize amplitude demodulation to wideband signals. We pose demodulation as a recovery problem of an oversampled corrupted signal and introduce special iterative schemes belonging to the family of alternating projection algorithms to solve it. Sensibly chosen structural assumptions on the demodulation outputs allow us to reveal the high inferential accuracy of the method over a rich set of relevant signals. This new approach surpasses current state-of-the-art demodulation techniques apt to wideband signals in computational efficiency by up to many orders of magnitude with no sacrifice in quality. Such performance opens the door for applications of the amplitude demodulation procedure in new contexts. In particular, the new method makes online and large-scale offline data processing feasible, including the calculation of modulator-carrier pairs in higher dimensions and poor sampling conditions, independent of the signal bandwidth. We illustrate the utility and specifics of applications of the new method in practice by using natural speech and synthetic signals.","lang":"eng"}],"publication":"IEEE Transactions on Signal Processing","doi":"10.1109/TSP.2021.3087899","title":"Fast and accurate amplitude demodulation of wideband signals","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://arxiv.org/abs/2102.04832","open_access":"1"}]},{"date_updated":"2023-08-11T10:55:08Z","author":[{"full_name":"Baranov, Dmitry","last_name":"Baranov","first_name":"Dmitry"},{"full_name":"Šverko, Tara","last_name":"Šverko","first_name":"Tara"},{"first_name":"Taylor","last_name":"Moot","full_name":"Moot, Taylor"},{"first_name":"Helena R.","last_name":"Keller","full_name":"Keller, Helena R."},{"last_name":"Klein","first_name":"Megan D.","full_name":"Klein, Megan D."},{"first_name":"E. K.","last_name":"Vishnu","full_name":"Vishnu, E. K."},{"first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs","full_name":"Balazs, Daniel","orcid":"0000-0001-7597-043X"},{"full_name":"Shulenberger, Katherine E.","last_name":"Shulenberger","first_name":"Katherine E."}],"article_type":"original","date_created":"2021-08-08T22:01:31Z","_id":"9829","acknowledgement":"K. E. Shulenberger, M. D. Klein, T. Šverko, and H. R. Keller would like to thank Professors Moungi Bawendi (MIT) and Gordana Dukovic (CU Boulder) for their feedback and support of the News in Nanocrystals initiative. The authors thank Madison Jilek (CU Boulder) and Dhananjeya Kumaar (ETH Zurich) for their help in the organization of the seminar, and Professors Brandi Cossairt (University of Washington) and Gordana Dukovic for their feedback on an earlier version of this manuscript. The authors thank all the seminar speakers and attendees for their interest and continuing participation in the seminar series.","volume":15,"issue":"7","scopus_import":"1","citation":{"ista":"Baranov D, Šverko T, Moot T, Keller HR, Klein MD, Vishnu EK, Balazs D, Shulenberger KE. 2021. News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. ACS Nano. 15(7), 10743–10747.","ama":"Baranov D, Šverko T, Moot T, et al. News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. <i>ACS Nano</i>. 2021;15(7):10743–10747. doi:<a href=\"https://doi.org/10.1021/acsnano.1c03276\">10.1021/acsnano.1c03276</a>","chicago":"Baranov, Dmitry, Tara Šverko, Taylor Moot, Helena R. Keller, Megan D. Klein, E. K. Vishnu, Daniel Balazs, and Katherine E. Shulenberger. “News in Nanocrystals Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible Nanoscience.” <i>ACS Nano</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsnano.1c03276\">https://doi.org/10.1021/acsnano.1c03276</a>.","short":"D. Baranov, T. Šverko, T. Moot, H.R. Keller, M.D. Klein, E.K. Vishnu, D. Balazs, K.E. Shulenberger, ACS Nano 15 (2021) 10743–10747.","mla":"Baranov, Dmitry, et al. “News in Nanocrystals Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible Nanoscience.” <i>ACS Nano</i>, vol. 15, no. 7, American Chemical Society, 2021, pp. 10743–10747, doi:<a href=\"https://doi.org/10.1021/acsnano.1c03276\">10.1021/acsnano.1c03276</a>.","apa":"Baranov, D., Šverko, T., Moot, T., Keller, H. R., Klein, M. D., Vishnu, E. K., … Shulenberger, K. E. (2021). News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.1c03276\">https://doi.org/10.1021/acsnano.1c03276</a>","ieee":"D. Baranov <i>et al.</i>, “News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience,” <i>ACS Nano</i>, vol. 15, no. 7. American Chemical Society, pp. 10743–10747, 2021."},"external_id":{"isi":["000679406500002"],"pmid":["34228432"]},"isi":1,"pmid":1,"department":[{"_id":"MaIb"}],"month":"07","intvolume":"        15","day":"06","date_published":"2021-07-06T00:00:00Z","publication_status":"published","year":"2021","publication_identifier":{"eissn":["1936086X"],"issn":["19360851"]},"page":"10743–10747","quality_controlled":"1","publisher":"American Chemical Society","language":[{"iso":"eng"}],"article_processing_charge":"No","oa":1,"oa_version":"Published Version","status":"public","doi":"10.1021/acsnano.1c03276","publication":"ACS Nano","abstract":[{"text":"In 2020, many in-person scientific events were canceled due to the COVID-19 pandemic, creating a vacuum in networking and knowledge exchange between scientists. To fill this void in scientific communication, a group of early career nanocrystal enthusiasts launched the virtual seminar series, News in Nanocrystals, in the summer of 2020. By the end of the year, the series had attracted over 850 participants from 46 countries. In this Nano Focus, we describe the process of organizing the News in Nanocrystals seminar series; discuss its growth, emphasizing what the organizers have learned in terms of diversity and accessibility; and provide an outlook for the next steps and future opportunities. This summary and analysis of experiences and learned lessons are intended to inform the broader scientific community, especially those who are looking for avenues to continue fostering discussion and scientific engagement virtually, both during the pandemic and after.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1021/acsnano.1c03276","open_access":"1"}],"title":"News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article"},{"isi":1,"pmid":1,"month":"08","department":[{"_id":"SaSi"}],"intvolume":"        12","day":"10","citation":{"short":"A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen, L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas, C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H. van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).","apa":"Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen, D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-25211-4\">https://doi.org/10.1038/s41467-021-25211-4</a>","mla":"Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” <i>Nature Communications</i>, vol. 12, 4808, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-25211-4\">10.1038/s41467-021-25211-4</a>.","ama":"Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-25211-4\">10.1038/s41467-021-25211-4</a>","ista":"Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. 12, 4808.","chicago":"Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-25211-4\">https://doi.org/10.1038/s41467-021-25211-4</a>.","ieee":"A. Raso <i>et al.</i>, “A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021."},"scopus_import":"1","external_id":{"isi":["000683910200042"],"pmid":["34376683"]},"date_created":"2021-08-10T11:49:20Z","_id":"9874","acknowledgement":"E.D. is supported by a VENI award 916-150-16 from the Netherlands Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship (EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number 627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência, Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART).","volume":12,"file_date_updated":"2021-08-10T12:29:59Z","date_updated":"2023-08-11T10:27:03Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","author":[{"last_name":"Raso","first_name":"Andrea","full_name":"Raso, Andrea"},{"full_name":"Dirkx, Ellen","first_name":"Ellen","last_name":"Dirkx"},{"full_name":"Sampaio-Pinto, Vasco","last_name":"Sampaio-Pinto","first_name":"Vasco"},{"last_name":"el Azzouzi","first_name":"Hamid","full_name":"el Azzouzi, Hamid"},{"orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J","first_name":"Ryan J","last_name":"Cubero","id":"850B2E12-9CD4-11E9-837F-E719E6697425"},{"last_name":"Sorensen","first_name":"Daniel W.","full_name":"Sorensen, Daniel W."},{"full_name":"Ottaviani, Lara","first_name":"Lara","last_name":"Ottaviani"},{"full_name":"Olieslagers, Servé","first_name":"Servé","last_name":"Olieslagers"},{"full_name":"Huibers, Manon M.","last_name":"Huibers","first_name":"Manon M."},{"first_name":"Roel","last_name":"de Weger","full_name":"de Weger, Roel"},{"full_name":"Siddiqi, Sailay","first_name":"Sailay","last_name":"Siddiqi"},{"first_name":"Silvia","last_name":"Moimas","full_name":"Moimas, Silvia"},{"first_name":"Consuelo","last_name":"Torrini","full_name":"Torrini, Consuelo"},{"full_name":"Zentillin, Lorena","first_name":"Lorena","last_name":"Zentillin"},{"first_name":"Luca","last_name":"Braga","full_name":"Braga, Luca"},{"last_name":"Nascimento","first_name":"Diana S.","full_name":"Nascimento, Diana S."},{"last_name":"da Costa Martins","first_name":"Paula A.","full_name":"da Costa Martins, Paula A."},{"first_name":"Jop H.","last_name":"van Berlo","full_name":"van Berlo, Jop H."},{"full_name":"Zacchigna, Serena","last_name":"Zacchigna","first_name":"Serena"},{"full_name":"Giacca, Mauro","first_name":"Mauro","last_name":"Giacca"},{"full_name":"De Windt, Leon J.","last_name":"De Windt","first_name":"Leon J."}],"ddc":["610","570"],"file":[{"date_created":"2021-08-10T12:29:59Z","relation":"main_file","checksum":"48d8562e8229e4282f3f354b329722c5","creator":"asandaue","access_level":"open_access","content_type":"application/pdf","date_updated":"2021-08-10T12:29:59Z","success":1,"file_name":"2021_NatureCommunications_Raso.pdf","file_id":"9876","file_size":4364333}],"title":"A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-021-25211-4","abstract":[{"lang":"eng","text":"Myocardial regeneration is restricted to early postnatal life, when mammalian cardiomyocytes still retain the ability to proliferate. The molecular cues that induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster is higher expressed in the early postnatal myocardium and decreases in expression towards adulthood, especially under conditions of overload, and orchestrates the transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse heart provokes cardiomyocyte proliferation by targeting a network of negative cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated remodeling to overload by derepression of the prohypertrophic transcription factors Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25 provokes nearly complete regeneration of the adult myocardium after ischemic injury. Our data demonstrate that exploitation of conserved molecular programs can enhance the regenerative capacity of the injured heart."}],"publication":"Nature Communications","article_processing_charge":"Yes","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-32785-0"}]},"language":[{"iso":"eng"}],"article_number":"4808","oa_version":"Published Version","genbank":["GSE178867"],"status":"public","has_accepted_license":"1","oa":1,"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","year":"2021","date_published":"2021-08-10T00:00:00Z","quality_controlled":"1","publisher":"Springer Nature"},{"scopus_import":"1","citation":{"mla":"Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>.","apa":"Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma, R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>","short":"J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 118 (2021).","ama":"Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(29). doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>","chicago":"Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>.","ista":"Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. 118(29), e2104445118.","ieee":"J. A. Rodrigues <i>et al.</i>, “Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting,” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 29. National Academy of Sciences, 2021."},"external_id":{"pmid":["34272287"],"isi":["000685037700012"]},"month":"07","department":[{"_id":"DaZi"}],"pmid":1,"isi":1,"day":"16","intvolume":"       118","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_updated":"2023-08-11T10:28:10Z","article_type":"original","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"last_name":"Rodrigues","first_name":"Jessica A.","full_name":"Rodrigues, Jessica A."},{"full_name":"Hsieh, Ping-Hung","last_name":"Hsieh","first_name":"Ping-Hung"},{"first_name":"Deling","last_name":"Ruan","full_name":"Ruan, Deling"},{"first_name":"Toshiro","last_name":"Nishimura","full_name":"Nishimura, Toshiro"},{"first_name":"Manoj K.","last_name":"Sharma","full_name":"Sharma, Manoj K."},{"full_name":"Sharma, Rita","last_name":"Sharma","first_name":"Rita"},{"last_name":"Ye","first_name":"XinYi","full_name":"Ye, XinYi"},{"full_name":"Nguyen, Nicholas D.","last_name":"Nguyen","first_name":"Nicholas D."},{"full_name":"Nijjar, Sukhranjan","first_name":"Sukhranjan","last_name":"Nijjar"},{"full_name":"Ronald, Pamela C.","first_name":"Pamela C.","last_name":"Ronald"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"_id":"9877","date_created":"2021-08-10T19:30:41Z","issue":"29","file_date_updated":"2021-08-11T09:31:41Z","volume":118,"acknowledgement":"We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing team for generating the IR64 genome sequence and initial analysis; L. Bartley and E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University of California (UC), Berkeley Sanger sequencing team for technical advice and service. This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.","doi":"10.1073/pnas.2104445118","publication":"Proceedings of the National Academy of Sciences","abstract":[{"lang":"eng","text":"Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution."}],"ddc":["580","570"],"file":[{"file_size":1898360,"file_id":"9879","date_updated":"2021-08-11T09:31:41Z","success":1,"file_name":"2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf","creator":"asandaue","access_level":"open_access","content_type":"application/pdf","checksum":"19e84ad8c03c60222744ee8e16cd6998","date_created":"2021-08-11T09:31:41Z","relation":"main_file"}],"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting","date_published":"2021-07-16T00:00:00Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","year":"2021","publisher":"National Academy of Sciences","quality_controlled":"1","article_number":"e2104445118","language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","oa":1,"has_accepted_license":"1","status":"public","oa_version":"Published Version"},{"pmid":1,"isi":1,"month":"12","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"intvolume":"       118","day":"14","project":[{"call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>.","ista":"Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences. 118(51), e2113046118.","ama":"Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(51). doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>","mla":"Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>.","apa":"Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>","short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences 118 (2021).","ieee":"A. J. Johnson <i>et al.</i>, “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 51. National Academy of Sciences, 2021."},"external_id":{"isi":["000736417600043"],"pmid":["34907016"]},"date_created":"2021-08-11T14:11:43Z","_id":"9887","volume":118,"acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","file_date_updated":"2021-12-15T08:59:40Z","issue":"51","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2024-02-19T11:06:09Z","author":[{"orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dahhan, Dana A","last_name":"Dahhan","first_name":"Dana A"},{"first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh","full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509"},{"last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"first_name":"Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa"},{"orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso"},{"first_name":"Pierre","last_name":"Mahou","full_name":"Mahou, Pierre"},{"full_name":"Hrtyan, Mónika","last_name":"Hrtyan","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika"},{"last_name":"Wang","first_name":"Jie","full_name":"Wang, Jie"},{"full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","last_name":"Aguilera Servin","first_name":"Juan L"},{"last_name":"van Damme","first_name":"Daniël","full_name":"van Damme, Daniël"},{"last_name":"Beaurepaire","first_name":"Emmanuel","full_name":"Beaurepaire, Emmanuel"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"},{"last_name":"Bednarek","first_name":"Sebastian Y","full_name":"Bednarek, Sebastian Y"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"article_type":"original","ddc":["580"],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"file":[{"file_id":"10546","success":1,"file_name":"2021_PNAS_Johnson.pdf","date_updated":"2021-12-15T08:59:40Z","file_size":2757340,"date_created":"2021-12-15T08:59:40Z","relation":"main_file","content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","checksum":"8d01e72e22c4fb1584e72d8601947069"}],"title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1073/pnas.2113046118","publication":"Proceedings of the National Academy of Sciences","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells."}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"14510","status":"public"},{"relation":"research_data","id":"14988","status":"public"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2021.04.26.441441"}]},"article_number":"e2113046118","article_processing_charge":"No","has_accepted_license":"1","oa":1,"oa_version":"Published Version","status":"public","date_published":"2021-12-14T00:00:00Z","year":"2021","publication_status":"published","publication_identifier":{"eissn":["1091-6490"]},"quality_controlled":"1","publisher":"National Academy of Sciences"},{"title":"Floating Wigner crystal and periodic jellium configurations","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":4352640,"file_id":"10188","success":1,"file_name":"2021_JMathPhy_Lauritsen.pdf","date_updated":"2021-10-27T12:57:06Z","creator":"cziletti","access_level":"open_access","content_type":"application/pdf","checksum":"d035be2b894c4d50d90ac5ce252e27cd","date_created":"2021-10-27T12:57:06Z","relation":"main_file"}],"ddc":["530"],"abstract":[{"lang":"eng","text":"Extending on ideas of Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)], we present a modified “floating crystal” trial state for jellium (also known as the classical homogeneous electron gas) with density equal to a characteristic function. This allows us to show that three definitions of the jellium energy coincide in dimensions d ≥ 2, thus extending the result of Cotar and Petrache [“Equality of the Jellium and uniform electron gas next-order asymptotic terms for Coulomb and Riesz potentials,” arXiv: 1707.07664 (2019)] and Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)] that the three definitions coincide in dimension d ≥ 3. We show that the jellium energy is also equivalent to a “renormalized energy” studied in a series of papers by Serfaty and others, and thus, by the work of Bétermin and Sandier [Constr. Approximation 47, 39–74 (2018)], we relate the jellium energy to the order n term in the logarithmic energy of n points on the unit 2-sphere. We improve upon known lower bounds for this renormalized energy. Additionally, we derive formulas for the jellium energy of periodic configurations."}],"publication":"Journal of Mathematical Physics","doi":"10.1063/5.0053494","oa_version":"Published Version","status":"public","has_accepted_license":"1","oa":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"article_number":"083305","quality_controlled":"1","publisher":"AIP Publishing","year":"2021","publication_identifier":{"eissn":["1089-7658"],"issn":["0022-2488"]},"publication_status":"published","date_published":"2021-08-01T00:00:00Z","intvolume":"        62","day":"01","arxiv":1,"isi":1,"month":"08","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"external_id":{"isi":["000683960800003"],"arxiv":["2103.07975"]},"citation":{"mla":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” <i>Journal of Mathematical Physics</i>, vol. 62, no. 8, 083305, AIP Publishing, 2021, doi:<a href=\"https://doi.org/10.1063/5.0053494\">10.1063/5.0053494</a>.","apa":"Lauritsen, A. B. (2021). Floating Wigner crystal and periodic jellium configurations. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0053494\">https://doi.org/10.1063/5.0053494</a>","short":"A.B. Lauritsen, Journal of Mathematical Physics 62 (2021).","ista":"Lauritsen AB. 2021. Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. 62(8), 083305.","ama":"Lauritsen AB. Floating Wigner crystal and periodic jellium configurations. <i>Journal of Mathematical Physics</i>. 2021;62(8). doi:<a href=\"https://doi.org/10.1063/5.0053494\">10.1063/5.0053494</a>","chicago":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2021. <a href=\"https://doi.org/10.1063/5.0053494\">https://doi.org/10.1063/5.0053494</a>.","ieee":"A. B. Lauritsen, “Floating Wigner crystal and periodic jellium configurations,” <i>Journal of Mathematical Physics</i>, vol. 62, no. 8. AIP Publishing, 2021."},"scopus_import":"1","acknowledgement":"The author would like to thank Robert Seiringer for guidance and many helpful comments on this project. The author would also like to thank Mathieu Lewin for his comments on the manuscript and Lorenzo Portinale for providing his lecture notes for the course “Mathematics of quantum many-body systems” in spring 2020, taught by Robert Seiringer. The Proof of Theorem III.1 is inspired by these lecture notes.","volume":62,"issue":"8","file_date_updated":"2021-10-27T12:57:06Z","date_created":"2021-08-12T07:08:36Z","_id":"9891","author":[{"full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard"}],"keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-11T10:29:48Z"},{"arxiv":1,"day":"06","intvolume":"       127","department":[{"_id":"MaSe"},{"_id":"GradSch"},{"_id":"MiLe"}],"month":"08","isi":1,"external_id":{"isi":["000684276000002"],"arxiv":["2102.13633"]},"project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"850899"}],"citation":{"ieee":"V. Karle, M. Serbyn, and A. Michailidis, “Area-law entangled eigenstates from nullspaces of local Hamiltonians,” <i>Physical Review Letters</i>, vol. 127, no. 6. American Physical Society, 2021.","apa":"Karle, V., Serbyn, M., &#38; Michailidis, A. (2021). Area-law entangled eigenstates from nullspaces of local Hamiltonians. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.127.060602\">https://doi.org/10.1103/physrevlett.127.060602</a>","mla":"Karle, Volker, et al. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” <i>Physical Review Letters</i>, vol. 127, no. 6, 060602, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.127.060602\">10.1103/physrevlett.127.060602</a>.","short":"V. Karle, M. Serbyn, A. Michailidis, Physical Review Letters 127 (2021).","chicago":"Karle, Volker, Maksym Serbyn, and Alexios Michailidis. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.127.060602\">https://doi.org/10.1103/physrevlett.127.060602</a>.","ista":"Karle V, Serbyn M, Michailidis A. 2021. Area-law entangled eigenstates from nullspaces of local Hamiltonians. Physical Review Letters. 127(6), 060602.","ama":"Karle V, Serbyn M, Michailidis A. Area-law entangled eigenstates from nullspaces of local Hamiltonians. <i>Physical Review Letters</i>. 2021;127(6). doi:<a href=\"https://doi.org/10.1103/physrevlett.127.060602\">10.1103/physrevlett.127.060602</a>"},"file_date_updated":"2021-08-13T09:28:08Z","issue":"6","acknowledgement":"We acknowledge useful discussions with V. Gritsev and A. Garkun and suggestions on implementation of the\r\nPPXPP model by D. Bluvstein. A. M. and M. S. were supported by the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899)","volume":127,"_id":"9903","date_created":"2021-08-13T09:27:39Z","author":[{"orcid":"0000-0002-6963-0129","full_name":"Karle, Volker","first_name":"Volker","last_name":"Karle","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425"},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064"}],"article_type":"letter_note","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-11T10:43:27Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","title":"Area-law entangled eigenstates from nullspaces of local Hamiltonians","ddc":["539"],"file":[{"file_size":5064231,"date_updated":"2021-08-13T09:28:08Z","success":1,"file_name":"PhysRevLett.127.060602_SOM.pdf","file_id":"9904","checksum":"51218f302dcef99d90d1209809fcc874","creator":"mserbyn","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-08-13T09:28:08Z"}],"publication":"Physical Review Letters","abstract":[{"text":"Eigenstate thermalization in quantum many-body systems implies that eigenstates at high energy are similar to random vectors. Identifying systems where at least some eigenstates are nonthermal is an outstanding question. In this Letter we show that interacting quantum models that have a nullspace—a degenerate subspace of eigenstates at zero energy (zero modes), which corresponds to infinite temperature, provide a route to nonthermal eigenstates. We analytically show the existence of a zero mode which can be represented as a matrix product state for a certain class of local Hamiltonians. In the more general case we use a subspace disentangling algorithm to generate an orthogonal basis of zero modes characterized by increasing entanglement entropy. We show evidence for an area-law entanglement scaling of the least-entangled zero mode in the broad parameter regime, leading to a conjecture that all local Hamiltonians with the nullspace feature zero modes with area-law entanglement scaling and, as such, break the strong thermalization hypothesis. Finally, we find zero modes in constrained models and propose a setup for observing their experimental signatures.","lang":"eng"}],"doi":"10.1103/physrevlett.127.060602","oa":1,"has_accepted_license":"1","status":"public","oa_version":"Published Version","article_number":"060602","ec_funded":1,"language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","publisher":"American Physical Society","quality_controlled":"1","date_published":"2021-08-06T00:00:00Z","publication_status":"published","year":"2021","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]}},{"acknowledgement":"We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta, Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España for useful comments. The opinions expressed in this document are exclusively of the authors and, therefore, do not necessarily coincide with those of the Banco de España or the Eurosystem. ETD is supported by the Swiss National Science and Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator Grant (771209-CharFL).","volume":11,"issue":"1","file_date_updated":"2021-08-16T11:36:49Z","date_created":"2021-08-15T22:01:26Z","_id":"9905","author":[{"full_name":"Rella, Simon","first_name":"Simon","last_name":"Rella","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425"},{"last_name":"Kulikova","first_name":"Yuliya A.","full_name":"Kulikova, Yuliya A."},{"full_name":"Dermitzakis, Emmanouil T.","last_name":"Dermitzakis","first_name":"Emmanouil T."},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-11T10:42:58Z","intvolume":"        11","day":"30","isi":1,"pmid":1,"department":[{"_id":"FyKo"}],"month":"07","external_id":{"isi":["000683329100001"],"pmid":["34330988"]},"project":[{"name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209","call_identifier":"H2020"}],"scopus_import":"1","citation":{"ista":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 11(1), 15729.","chicago":"Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-95025-3\">https://doi.org/10.1038/s41598-021-95025-3</a>.","ama":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. <i>Scientific Reports</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.1038/s41598-021-95025-3\">10.1038/s41598-021-95025-3</a>","apa":"Rella, S., Kulikova, Y. A., Dermitzakis, E. T., &#38; Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-021-95025-3\">https://doi.org/10.1038/s41598-021-95025-3</a>","short":"S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021).","mla":"Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” <i>Scientific Reports</i>, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-021-95025-3\">10.1038/s41598-021-95025-3</a>.","ieee":"S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,” <i>Scientific Reports</i>, vol. 11, no. 1. Springer Nature, 2021."},"has_accepted_license":"1","oa":1,"oa_version":"Published Version","status":"public","related_material":{"link":[{"url":"https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/","description":"News on IST Website","relation":"press_release"}]},"language":[{"iso":"eng"}],"ec_funded":1,"article_number":"15729","article_processing_charge":"Yes","quality_controlled":"1","publisher":"Springer Nature","date_published":"2021-07-30T00:00:00Z","publication_identifier":{"eissn":["20452322"]},"publication_status":"published","year":"2021","title":"Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","ddc":["570","610"],"file":[{"date_updated":"2021-08-16T11:36:49Z","success":1,"file_name":"2021_ScientificReports_Rella.pdf","file_id":"9927","file_size":3432001,"relation":"main_file","date_created":"2021-08-16T11:36:49Z","checksum":"ac86892ed17e6724c7251844da5cef5c","creator":"asandaue","access_level":"open_access","content_type":"application/pdf"}],"publication":"Scientific Reports","abstract":[{"lang":"eng","text":"Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period."}],"doi":"10.1038/s41598-021-95025-3"},{"publication":"International Journal of Molecular Sciences","abstract":[{"lang":"eng","text":"Endometriosis is a common gynecological disorder characterized by ectopic growth of endometrium outside the uterus and is associated with chronic pain and infertility. We investigated the role of the long intergenic noncoding RNA 01133 (LINC01133) in endometriosis, an lncRNA that has been implicated in several types of cancer. We found that LINC01133 is upregulated in ectopic endometriotic lesions. As expression appeared higher in the epithelial endometrial layer, we performed a siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic assays indicated that LINC01133 may promote proliferation and suppress cellular migration, and affect the cytoskeleton and morphology of the cells. Gene ontology analysis of differentially expressed genes indicated that cell proliferation and migration pathways were affected in line with the observed phenotype. We validated upregulation of p21 and downregulation of Cyclin A at the protein level, which together with the quantification of the DNA content using fluorescence-activated cell sorting (FACS) analysis indicated that the observed effects on cellular proliferation may be due to changes in cell cycle. Further, we found testis-specific protein kinase 1 (TESK1) kinase upregulation corresponding with phosphorylation and inactivation of actin severing protein Cofilin, which could explain changes in the cytoskeleton and cellular migration. These results indicate that endometriosis is associated with LINC01133 upregulation, which may affect pathogenesis via the cellular proliferation and migration pathways."}],"doi":"10.3390/ijms22168385","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line","ddc":["570"],"file":[{"access_level":"open_access","creator":"asandaue","content_type":"application/pdf","checksum":"be7f0042607ca60549cb27513c19c6af","date_created":"2021-08-16T09:29:17Z","relation":"main_file","file_size":2646018,"file_id":"9922","file_name":"2021_InternationalJournalOfMolecularSciences_Yotova.pdf","success":1,"date_updated":"2021-08-16T09:29:17Z"}],"publisher":"MDPI","quality_controlled":"1","date_published":"2021-08-04T00:00:00Z","publication_status":"published","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"year":"2021","oa":1,"has_accepted_license":"1","status":"public","oa_version":"Published Version","article_number":"8385","language":[{"iso":"eng"}],"article_processing_charge":"Yes","external_id":{"isi":["000689147400001"]},"scopus_import":"1","citation":{"chicago":"Yotova, Iveta, Quanah J. Hudson, Florian Pauler, Katharina Proestling, Isabella Haslinger, Lorenz Kuessel, Alexandra Perricos, Heinrich Husslein, and René Wenzl. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22168385\">https://doi.org/10.3390/ijms22168385</a>.","ista":"Yotova I, Hudson QJ, Pauler F, Proestling K, Haslinger I, Kuessel L, Perricos A, Husslein H, Wenzl R. 2021. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. International Journal of Molecular Sciences. 22(16), 8385.","ama":"Yotova I, Hudson QJ, Pauler F, et al. LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. <i>International Journal of Molecular Sciences</i>. 2021;22(16). doi:<a href=\"https://doi.org/10.3390/ijms22168385\">10.3390/ijms22168385</a>","short":"I. Yotova, Q.J. Hudson, F. Pauler, K. Proestling, I. Haslinger, L. Kuessel, A. Perricos, H. Husslein, R. Wenzl, International Journal of Molecular Sciences 22 (2021).","apa":"Yotova, I., Hudson, Q. J., Pauler, F., Proestling, K., Haslinger, I., Kuessel, L., … Wenzl, R. (2021). LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22168385\">https://doi.org/10.3390/ijms22168385</a>","mla":"Yotova, Iveta, et al. “LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 16, 8385, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22168385\">10.3390/ijms22168385</a>.","ieee":"I. Yotova <i>et al.</i>, “LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 16. MDPI, 2021."},"day":"04","intvolume":"        22","department":[{"_id":"SiHi"}],"month":"08","isi":1,"article_type":"original","author":[{"full_name":"Yotova, Iveta","last_name":"Yotova","first_name":"Iveta"},{"full_name":"Hudson, Quanah J.","first_name":"Quanah J.","last_name":"Hudson"},{"first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"last_name":"Proestling","first_name":"Katharina","full_name":"Proestling, Katharina"},{"first_name":"Isabella","last_name":"Haslinger","full_name":"Haslinger, Isabella"},{"full_name":"Kuessel, Lorenz","first_name":"Lorenz","last_name":"Kuessel"},{"first_name":"Alexandra","last_name":"Perricos","full_name":"Perricos, Alexandra"},{"last_name":"Husslein","first_name":"Heinrich","full_name":"Husslein, Heinrich"},{"full_name":"Wenzl, René","last_name":"Wenzl","first_name":"René"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-11T10:34:13Z","file_date_updated":"2021-08-16T09:29:17Z","issue":"16","volume":22,"acknowledgement":"Open access funding provided by Medical University of Vienna. The authors would like to thank all the participants and health professionals involved in the present study. We want to thank our technical assistants Barbara Widmar and Matthias Witzmann-Stern for their diligent work and constant assistance. We would like to thank Simon Hippenmeyer for access to\r\nbioinformatic infrastructure and resources.","_id":"9906","date_created":"2021-08-15T22:01:27Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","title":"Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva","file":[{"access_level":"open_access","creator":"asandaue","content_type":"application/pdf","checksum":"a4bc06e9a2c803ceff5a91f10b174054","date_created":"2021-08-16T09:35:56Z","relation":"main_file","file_size":6132410,"file_id":"9923","success":1,"file_name":"2021_InternationalJournalOfMolecularSciences_Labajová .pdf","date_updated":"2021-08-16T09:35:56Z"}],"ddc":["570"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publication":"International Journal of Molecular Sciences","abstract":[{"lang":"eng","text":"DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane. "}],"doi":"10.3390/ijms22158350","oa":1,"has_accepted_license":"1","status":"public","oa_version":"Published Version","article_number":"8350","ec_funded":1,"language":[{"iso":"eng"}],"article_processing_charge":"Yes","publisher":"MDPI","quality_controlled":"1","date_published":"2021-08-01T00:00:00Z","publication_status":"published","year":"2021","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"day":"01","intvolume":"        22","department":[{"_id":"MaLo"}],"month":"08","pmid":1,"isi":1,"external_id":{"isi":["000681815400001"],"pmid":["34361115"]},"scopus_import":"1","project":[{"call_identifier":"H2020","grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell"}],"citation":{"ama":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. 2021;22(15). doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>","chicago":"Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>.","ista":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. 22(15), 8350.","short":"N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International Journal of Molecular Sciences 22 (2021).","apa":"Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., &#38; Barák, I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>","mla":"Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15, 8350, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>.","ieee":"N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák, “Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15. MDPI, 2021."},"issue":"15","file_date_updated":"2021-08-16T09:35:56Z","volume":22,"acknowledgement":"We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova and other members of Barák’s laboratory for useful discussions, suggestions and help. Special thanks also to Emília Chovancová for technical support. We are grateful to Juraj Labaj for drawing the model and for help with graphics. Many thanks to all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp Radler, and other members of the Loose’s laboratory for sharing their knowledge of SLB preparation and TIRF experiment chambers, for sharing coverslips and for help with the TIRF microscope and data analysis. We also thank the members of the Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J. Bauer for critically reading the manuscript.","_id":"9907","date_created":"2021-08-15T22:01:27Z","author":[{"full_name":"Labajová, Naďa","first_name":"Naďa","last_name":"Labajová"},{"last_name":"Baranova","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S.","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S."},{"first_name":"Miroslav","last_name":"Jurásek","full_name":"Jurásek, Miroslav"},{"full_name":"Vácha, Robert","first_name":"Robert","last_name":"Vácha"},{"first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"},{"last_name":"Barák","first_name":"Imrich","full_name":"Barák, Imrich"}],"article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-11T10:34:44Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","title":"Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict","file":[{"file_id":"9926","success":1,"file_name":"2021_Genes_Picard.pdf","date_updated":"2021-08-16T09:49:35Z","file_size":2297655,"date_created":"2021-08-16T09:49:35Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"asandaue","checksum":"744e60e56d290a96da3c91a9779f886f"}],"ddc":["570"],"publication":"Genes","abstract":[{"lang":"eng","text":"About eight million animal species are estimated to live on Earth, and all except those belonging to one subphylum are invertebrates. Invertebrates are incredibly diverse in their morphologies, life histories, and in the range of the ecological niches that they occupy. A great variety of modes of reproduction and sex determination systems is also observed among them, and their mosaic-distribution across the phylogeny shows that transitions between them occur frequently and rapidly. Genetic conflict in its various forms is a long-standing theory to explain what drives those evolutionary transitions. Here, we review (1) the different modes of reproduction among invertebrate species, highlighting sexual reproduction as the probable ancestral state; (2) the paradoxical diversity of sex determination systems; (3) the different types of genetic conflicts that could drive the evolution of such different systems."}],"doi":"10.3390/genes12081136","oa":1,"has_accepted_license":"1","status":"public","oa_version":"Published Version","ec_funded":1,"article_number":"1136","language":[{"iso":"eng"}],"article_processing_charge":"Yes","publisher":"MDPI","quality_controlled":"1","date_published":"2021-08-01T00:00:00Z","publication_status":"published","publication_identifier":{"eissn":["20734425"]},"year":"2021","day":"01","intvolume":"        12","month":"08","department":[{"_id":"BeVi"}],"isi":1,"external_id":{"isi":["000690475900001"]},"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","call_identifier":"H2020"}],"scopus_import":"1","citation":{"ieee":"M. A. L. Picard, B. Vicoso, S. Bertrand, and H. Escriva, “Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict,” <i>Genes</i>, vol. 12, no. 8. MDPI, 2021.","short":"M.A.L. Picard, B. Vicoso, S. Bertrand, H. Escriva, Genes 12 (2021).","apa":"Picard, M. A. L., Vicoso, B., Bertrand, S., &#38; Escriva, H. (2021). Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12081136\">https://doi.org/10.3390/genes12081136</a>","mla":"Picard, Marion A. L., et al. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” <i>Genes</i>, vol. 12, no. 8, 1136, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12081136\">10.3390/genes12081136</a>.","chicago":"Picard, Marion A L, Beatriz Vicoso, Stéphanie Bertrand, and Hector Escriva. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12081136\">https://doi.org/10.3390/genes12081136</a>.","ama":"Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. <i>Genes</i>. 2021;12(8). doi:<a href=\"https://doi.org/10.3390/genes12081136\">10.3390/genes12081136</a>","ista":"Picard MAL, Vicoso B, Bertrand S, Escriva H. 2021. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. 12(8), 1136."},"issue":"8","file_date_updated":"2021-08-16T09:49:35Z","volume":12,"_id":"9908","date_created":"2021-08-15T22:01:27Z","article_type":"review","author":[{"first_name":"Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","full_name":"Picard, Marion A L","orcid":"0000-0002-8101-2518"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"first_name":"Stéphanie","last_name":"Bertrand","full_name":"Bertrand, Stéphanie"},{"full_name":"Escriva, Hector","first_name":"Hector","last_name":"Escriva"}],"date_updated":"2023-08-11T10:42:32Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"doi":"10.3390/genes12081141","abstract":[{"text":"Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at concentrations above 1 µM, suggesting that it was more selective in triggering a root inhibition response. Analysis of a series of phosphonamide and phosphonate pyrabactin analogs suggested that adventitious root formation and lateral root branching are differentially regulated by ABA signaling. ABA biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition.","lang":"eng"}],"publication":"Genes","ddc":["580","570"],"file":[{"checksum":"3d99535618cf9a5b14d264408fa52e97","creator":"asandaue","access_level":"open_access","content_type":"application/pdf","relation":"main_file","date_created":"2021-08-16T09:02:40Z","file_size":1340305,"success":1,"file_name":"2021_Genes_Zeng.pdf","date_updated":"2021-08-16T09:02:40Z","file_id":"9919"}],"title":"Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","publication_identifier":{"eissn":["20734425"]},"year":"2021","publication_status":"published","date_published":"2021-07-27T00:00:00Z","quality_controlled":"1","publisher":"MDPI","article_processing_charge":"Yes","language":[{"iso":"eng"}],"article_number":"1141","oa_version":"Published Version","status":"public","has_accepted_license":"1","oa":1,"citation":{"chicago":"Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>.","ista":"Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 12(8), 1141.","ama":"Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. 2021;12(8). doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>","apa":"Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon, I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>","mla":"Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>, vol. 12, no. 8, 1141, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>.","short":"Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon, P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).","ieee":"Y. Zeng <i>et al.</i>, “Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling,” <i>Genes</i>, vol. 12, no. 8. MDPI, 2021."},"scopus_import":"1","external_id":{"isi":["000690558000001"]},"isi":1,"department":[{"_id":"JiFr"}],"month":"07","intvolume":"        12","day":"27","date_updated":"2023-08-11T10:32:21Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_type":"original","author":[{"full_name":"Zeng, Yinwei","last_name":"Zeng","first_name":"Yinwei"},{"full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten"},{"full_name":"Trinh, Hoang Khai","first_name":"Hoang Khai","last_name":"Trinh"},{"first_name":"Thomas","last_name":"Heugebaert","full_name":"Heugebaert, Thomas"},{"full_name":"Stevens, Christian V.","first_name":"Christian V.","last_name":"Stevens"},{"full_name":"Garcia-Maquilon, Irene","first_name":"Irene","last_name":"Garcia-Maquilon"},{"full_name":"Rodriguez, Pedro L.","first_name":"Pedro L.","last_name":"Rodriguez"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Geelen, Danny","last_name":"Geelen","first_name":"Danny"}],"date_created":"2021-08-15T22:01:28Z","_id":"9909","volume":12,"acknowledgement":"We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis mutants and ABA signaling mutants.","issue":"8","file_date_updated":"2021-08-16T09:02:40Z"},{"abstract":[{"lang":"eng","text":"Adult height inspired the first biometrical and quantitative genetic studies and is a test-case trait for understanding heritability. The studies of height led to formulation of the classical polygenic model, that has a profound influence on the way we view and analyse complex traits. An essential part of the classical model is an assumption of additivity of effects and normality of the distribution of the residuals. However, it may be expected that the normal approximation will become insufficient in bigger studies. Here, we demonstrate that when the height of hundreds of thousands of individuals is analysed, the model complexity needs to be increased to include non-additive interactions between sex, environment and genes. Alternatively, the use of log-normal approximation allowed us to still use the additive effects model. These findings are important for future genetic and methodologic studies that make use of adult height as an exemplar trait."}],"publication":"European Journal of Human Genetics","doi":"10.1038/s41431-021-00836-7","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"The limits of normal approximation for adult height","file":[{"file_size":1079395,"file_id":"9921","file_name":"2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf","success":1,"date_updated":"2021-08-16T09:14:36Z","content_type":"application/pdf","creator":"asandaue","access_level":"open_access","checksum":"a676d76f91b0dbe0504c63e469129c2a","relation":"main_file","date_created":"2021-08-16T09:14:36Z"}],"ddc":["576"],"publisher":"Springer Nature","quality_controlled":"1","page":"1082-1091","publication_identifier":{"issn":["10184813"],"eissn":["14765438"]},"publication_status":"published","year":"2021","date_published":"2021-07-01T00:00:00Z","status":"public","oa_version":"Published Version","oa":1,"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","ec_funded":1,"language":[{"iso":"eng"}],"external_id":{"isi":["000625853200001"],"pmid":["33664501"]},"citation":{"chicago":"Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A. Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The Limits of Normal Approximation for Adult Height.” <i>European Journal of Human Genetics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41431-021-00836-7\">https://doi.org/10.1038/s41431-021-00836-7</a>.","ama":"Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation for adult height. <i>European Journal of Human Genetics</i>. 2021;29(7):1082-1091. doi:<a href=\"https://doi.org/10.1038/s41431-021-00836-7\">10.1038/s41431-021-00836-7</a>","ista":"Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European Journal of Human Genetics. 29(7), 1082–1091.","short":"S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich, F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.","apa":"Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich, T. I., Kondrashov, F., &#38; Aulchenko, Y. S. (2021). The limits of normal approximation for adult height. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-021-00836-7\">https://doi.org/10.1038/s41431-021-00836-7</a>","mla":"Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.” <i>European Journal of Human Genetics</i>, vol. 29, no. 7, Springer Nature, 2021, pp. 1082–91, doi:<a href=\"https://doi.org/10.1038/s41431-021-00836-7\">10.1038/s41431-021-00836-7</a>.","ieee":"S. A. Slavskii <i>et al.</i>, “The limits of normal approximation for adult height,” <i>European Journal of Human Genetics</i>, vol. 29, no. 7. Springer Nature, pp. 1082–1091, 2021."},"project":[{"call_identifier":"H2020","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","day":"01","intvolume":"        29","department":[{"_id":"FyKo"}],"month":"07","pmid":1,"isi":1,"author":[{"last_name":"Slavskii","first_name":"Sergei A.","full_name":"Slavskii, Sergei A."},{"full_name":"Kuznetsov, Ivan A.","last_name":"Kuznetsov","first_name":"Ivan A."},{"first_name":"Tatiana I.","last_name":"Shashkova","full_name":"Shashkova, Tatiana I."},{"full_name":"Bazykin, Georgii A.","first_name":"Georgii A.","last_name":"Bazykin"},{"full_name":"Axenovich, Tatiana I.","first_name":"Tatiana I.","last_name":"Axenovich"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"full_name":"Aulchenko, Yurii S.","first_name":"Yurii S.","last_name":"Aulchenko"}],"article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-11T10:33:42Z","file_date_updated":"2021-08-16T09:14:36Z","issue":"7","acknowledgement":"We are grateful to Marianna Bevova and Pavel Borodin for fruitful discussion and help with conceptualising our findings and to Lennart C. Karssen for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects in control of complex human traits”). The work of SAS, IAK, and TIS were supported by Russian Ministry of Science and Education under the 5–100 Excellence Programme. The work of YSA and TIA was supported by the Ministry of Education and Science of the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4). FAK is supported by the ERC Consolidator Grant (ChrFL: 771209).","volume":29,"_id":"9910","date_created":"2021-08-15T22:01:28Z"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jmi.13041"}],"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy","publication":"Journal of Microscopy","abstract":[{"lang":"eng","text":"A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics."}],"doi":"10.1111/jmi.13041","oa":1,"status":"public","oa_version":"Published Version","language":[{"iso":"eng"}],"article_processing_charge":"Yes","page":"56-73","publisher":"Wiley","quality_controlled":"1","date_published":"2021-08-11T00:00:00Z","publication_identifier":{"issn":["0022-2720"],"eissn":["1365-2818"]},"year":"2021","publication_status":"published","day":"11","intvolume":"       284","month":"08","department":[{"_id":"Bio"}],"isi":1,"external_id":{"isi":["000683702700001"]},"scopus_import":"1","citation":{"ieee":"G. Nelson <i>et al.</i>, “QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy,” <i>Journal of Microscopy</i>, vol. 284, no. 1. Wiley, pp. 56–73, 2021.","ista":"Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 284(1), 56–73.","ama":"Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. <i>Journal of Microscopy</i>. 2021;284(1):56-73. doi:<a href=\"https://doi.org/10.1111/jmi.13041\">10.1111/jmi.13041</a>","chicago":"Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” <i>Journal of Microscopy</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jmi.13041\">https://doi.org/10.1111/jmi.13041</a>.","mla":"Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” <i>Journal of Microscopy</i>, vol. 284, no. 1, Wiley, 2021, pp. 56–73, doi:<a href=\"https://doi.org/10.1111/jmi.13041\">10.1111/jmi.13041</a>.","short":"G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin, I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L. Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck, A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia, J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann, A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch, J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa, A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli, A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich, G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler, M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins, D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami, A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj, A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz, M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer, C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73.","apa":"Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M., … Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. <i>Journal of Microscopy</i>. Wiley. <a href=\"https://doi.org/10.1111/jmi.13041\">https://doi.org/10.1111/jmi.13041</a>"},"issue":"1","acknowledgement":"We thank https://www.somersault1824.com/somersault18:24 BV (Leuven, Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122, in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.","volume":284,"_id":"9911","date_created":"2021-08-15T22:01:29Z","article_type":"original","author":[{"first_name":"Glyn","last_name":"Nelson","full_name":"Nelson, Glyn"},{"full_name":"Boehm, Ulrike","last_name":"Boehm","first_name":"Ulrike"},{"first_name":"Steve","last_name":"Bagley","full_name":"Bagley, Steve"},{"first_name":"Peter","last_name":"Bajcsy","full_name":"Bajcsy, Peter"},{"full_name":"Bischof, Johanna","last_name":"Bischof","first_name":"Johanna"},{"full_name":"Brown, Claire M.","last_name":"Brown","first_name":"Claire M."},{"full_name":"Dauphin, Aurélien","first_name":"Aurélien","last_name":"Dauphin"},{"last_name":"Dobbie","first_name":"Ian M.","full_name":"Dobbie, Ian M."},{"full_name":"Eriksson, John E.","last_name":"Eriksson","first_name":"John E."},{"full_name":"Faklaris, Orestis","first_name":"Orestis","last_name":"Faklaris"},{"full_name":"Fernandez-Rodriguez, Julia","last_name":"Fernandez-Rodriguez","first_name":"Julia"},{"full_name":"Ferrand, Alexia","first_name":"Alexia","last_name":"Ferrand"},{"full_name":"Gelman, Laurent","last_name":"Gelman","first_name":"Laurent"},{"last_name":"Gheisari","first_name":"Ali","full_name":"Gheisari, Ali"},{"last_name":"Hartmann","first_name":"Hella","full_name":"Hartmann, Hella"},{"full_name":"Kukat, Christian","last_name":"Kukat","first_name":"Christian"},{"full_name":"Laude, Alex","last_name":"Laude","first_name":"Alex"},{"first_name":"Miso","last_name":"Mitkovski","full_name":"Mitkovski, Miso"},{"full_name":"Munck, Sebastian","last_name":"Munck","first_name":"Sebastian"},{"last_name":"North","first_name":"Alison J.","full_name":"North, Alison J."},{"first_name":"Tobias M.","last_name":"Rasse","full_name":"Rasse, Tobias M."},{"last_name":"Resch-Genger","first_name":"Ute","full_name":"Resch-Genger, Ute"},{"full_name":"Schuetz, Lucas C.","last_name":"Schuetz","first_name":"Lucas C."},{"full_name":"Seitz, Arne","first_name":"Arne","last_name":"Seitz"},{"full_name":"Strambio-De-Castillia, Caterina","last_name":"Strambio-De-Castillia","first_name":"Caterina"},{"full_name":"Swedlow, Jason R.","last_name":"Swedlow","first_name":"Jason R."},{"full_name":"Alexopoulos, Ioannis","first_name":"Ioannis","last_name":"Alexopoulos"},{"full_name":"Aumayr, Karin","last_name":"Aumayr","first_name":"Karin"},{"last_name":"Avilov","first_name":"Sergiy","full_name":"Avilov, Sergiy"},{"full_name":"Bakker, Gert Jan","last_name":"Bakker","first_name":"Gert Jan"},{"full_name":"Bammann, Rodrigo R.","first_name":"Rodrigo R.","last_name":"Bammann"},{"full_name":"Bassi, Andrea","last_name":"Bassi","first_name":"Andrea"},{"full_name":"Beckert, Hannes","first_name":"Hannes","last_name":"Beckert"},{"first_name":"Sebastian","last_name":"Beer","full_name":"Beer, Sebastian"},{"last_name":"Belyaev","first_name":"Yury","full_name":"Belyaev, Yury"},{"full_name":"Bierwagen, Jakob","first_name":"Jakob","last_name":"Bierwagen"},{"last_name":"Birngruber","first_name":"Konstantin A.","full_name":"Birngruber, Konstantin A."},{"full_name":"Bosch, Manel","last_name":"Bosch","first_name":"Manel"},{"last_name":"Breitlow","first_name":"Juergen","full_name":"Breitlow, Juergen"},{"full_name":"Cameron, Lisa A.","first_name":"Lisa A.","last_name":"Cameron"},{"full_name":"Chalfoun, Joe","last_name":"Chalfoun","first_name":"Joe"},{"last_name":"Chambers","first_name":"James J.","full_name":"Chambers, James J."},{"first_name":"Chieh Li","last_name":"Chen","full_name":"Chen, Chieh Li"},{"full_name":"Conde-Sousa, Eduardo","last_name":"Conde-Sousa","first_name":"Eduardo"},{"full_name":"Corbett, Alexander D.","first_name":"Alexander D.","last_name":"Corbett"},{"full_name":"Cordelieres, Fabrice P.","last_name":"Cordelieres","first_name":"Fabrice P."},{"first_name":"Elaine Del","last_name":"Nery","full_name":"Nery, Elaine Del"},{"last_name":"Dietzel","first_name":"Ralf","full_name":"Dietzel, Ralf"},{"full_name":"Eismann, Frank","last_name":"Eismann","first_name":"Frank"},{"full_name":"Fazeli, Elnaz","last_name":"Fazeli","first_name":"Elnaz"},{"last_name":"Felscher","first_name":"Andreas","full_name":"Felscher, Andreas"},{"first_name":"Hans","last_name":"Fried","full_name":"Fried, Hans"},{"first_name":"Nathalie","last_name":"Gaudreault","full_name":"Gaudreault, Nathalie"},{"last_name":"Goh","first_name":"Wah Ing","full_name":"Goh, Wah Ing"},{"first_name":"Thomas","last_name":"Guilbert","full_name":"Guilbert, Thomas"},{"full_name":"Hadleigh, Roland","first_name":"Roland","last_name":"Hadleigh"},{"full_name":"Hemmerich, Peter","last_name":"Hemmerich","first_name":"Peter"},{"full_name":"Holst, Gerhard A.","first_name":"Gerhard A.","last_name":"Holst"},{"last_name":"Itano","first_name":"Michelle S.","full_name":"Itano, Michelle S."},{"last_name":"Jaffe","first_name":"Claudia B.","full_name":"Jaffe, Claudia B."},{"first_name":"Helena K.","last_name":"Jambor","full_name":"Jambor, Helena K."},{"last_name":"Jarvis","first_name":"Stuart C.","full_name":"Jarvis, Stuart C."},{"full_name":"Keppler, Antje","last_name":"Keppler","first_name":"Antje"},{"full_name":"Kirchenbuechler, David","last_name":"Kirchenbuechler","first_name":"David"},{"first_name":"Marcel","last_name":"Kirchner","full_name":"Kirchner, Marcel"},{"full_name":"Kobayashi, Norio","last_name":"Kobayashi","first_name":"Norio"},{"last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel"},{"last_name":"Kunis","first_name":"Susanne","full_name":"Kunis, Susanne"},{"full_name":"Lacoste, Judith","last_name":"Lacoste","first_name":"Judith"},{"last_name":"Marcello","first_name":"Marco","full_name":"Marcello, Marco"},{"first_name":"Gabriel G.","last_name":"Martins","full_name":"Martins, Gabriel G."},{"last_name":"Metcalf","first_name":"Daniel J.","full_name":"Metcalf, Daniel J."},{"last_name":"Mitchell","first_name":"Claire A.","full_name":"Mitchell, Claire A."},{"full_name":"Moore, Joshua","last_name":"Moore","first_name":"Joshua"},{"first_name":"Tobias","last_name":"Mueller","full_name":"Mueller, Tobias"},{"first_name":"Michael S.","last_name":"Nelson","full_name":"Nelson, Michael S."},{"first_name":"Stephen","last_name":"Ogg","full_name":"Ogg, Stephen"},{"first_name":"Shuichi","last_name":"Onami","full_name":"Onami, Shuichi"},{"first_name":"Alexandra L.","last_name":"Palmer","full_name":"Palmer, Alexandra L."},{"full_name":"Paul-Gilloteaux, Perrine","first_name":"Perrine","last_name":"Paul-Gilloteaux"},{"first_name":"Jaime A.","last_name":"Pimentel","full_name":"Pimentel, Jaime A."},{"full_name":"Plantard, Laure","first_name":"Laure","last_name":"Plantard"},{"full_name":"Podder, Santosh","first_name":"Santosh","last_name":"Podder"},{"first_name":"Elton","last_name":"Rexhepaj","full_name":"Rexhepaj, Elton"},{"first_name":"Arnaud","last_name":"Royon","full_name":"Royon, Arnaud"},{"last_name":"Saari","first_name":"Markku A.","full_name":"Saari, Markku A."},{"full_name":"Schapman, Damien","last_name":"Schapman","first_name":"Damien"},{"full_name":"Schoonderwoert, Vincent","last_name":"Schoonderwoert","first_name":"Vincent"},{"full_name":"Schroth-Diez, Britta","first_name":"Britta","last_name":"Schroth-Diez"},{"first_name":"Stanley","last_name":"Schwartz","full_name":"Schwartz, Stanley"},{"last_name":"Shaw","first_name":"Michael","full_name":"Shaw, Michael"},{"last_name":"Spitaler","first_name":"Martin","full_name":"Spitaler, Martin"},{"full_name":"Stoeckl, Martin T.","first_name":"Martin T.","last_name":"Stoeckl"},{"last_name":"Sudar","first_name":"Damir","full_name":"Sudar, Damir"},{"full_name":"Teillon, Jeremie","last_name":"Teillon","first_name":"Jeremie"},{"first_name":"Stefan","last_name":"Terjung","full_name":"Terjung, Stefan"},{"full_name":"Thuenauer, Roland","first_name":"Roland","last_name":"Thuenauer"},{"last_name":"Wilms","first_name":"Christian D.","full_name":"Wilms, Christian D."},{"full_name":"Wright, Graham D.","last_name":"Wright","first_name":"Graham D."},{"full_name":"Nitschke, Roland","first_name":"Roland","last_name":"Nitschke"}],"date_updated":"2023-08-11T10:30:40Z"},{"file_date_updated":"2022-05-12T12:50:27Z","volume":22,"acknowledgement":"The authors are very grateful to Yan Fyodorov for discussions on the physical background and for providing references, and to the anonymous referee for numerous valuable remarks.","_id":"9912","date_created":"2021-08-15T22:01:29Z","article_type":"original","author":[{"last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","first_name":"Torben H"},{"orcid":"0000-0002-7327-856X","full_name":"Nemish, Yuriy","first_name":"Yuriy","last_name":"Nemish","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-11T10:31:48Z","arxiv":1,"day":"01","intvolume":"        22","month":"12","department":[{"_id":"LaEr"}],"isi":1,"external_id":{"arxiv":["1911.05112"],"isi":["000681531500001"]},"project":[{"call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems"}],"scopus_import":"1","citation":{"ieee":"L. Erdös, T. H. Krüger, and Y. Nemish, “Scattering in quantum dots via noncommutative rational functions,” <i>Annales Henri Poincaré </i>, vol. 22. Springer Nature, pp. 4205–4269, 2021.","short":"L. Erdös, T.H. Krüger, Y. Nemish, Annales Henri Poincaré  22 (2021) 4205–4269.","mla":"Erdös, László, et al. “Scattering in Quantum Dots via Noncommutative Rational Functions.” <i>Annales Henri Poincaré </i>, vol. 22, Springer Nature, 2021, pp. 4205–4269, doi:<a href=\"https://doi.org/10.1007/s00023-021-01085-6\">10.1007/s00023-021-01085-6</a>.","apa":"Erdös, L., Krüger, T. H., &#38; Nemish, Y. (2021). Scattering in quantum dots via noncommutative rational functions. <i>Annales Henri Poincaré </i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-021-01085-6\">https://doi.org/10.1007/s00023-021-01085-6</a>","ista":"Erdös L, Krüger TH, Nemish Y. 2021. Scattering in quantum dots via noncommutative rational functions. Annales Henri Poincaré . 22, 4205–4269.","ama":"Erdös L, Krüger TH, Nemish Y. Scattering in quantum dots via noncommutative rational functions. <i>Annales Henri Poincaré </i>. 2021;22:4205–4269. doi:<a href=\"https://doi.org/10.1007/s00023-021-01085-6\">10.1007/s00023-021-01085-6</a>","chicago":"Erdös, László, Torben H Krüger, and Yuriy Nemish. “Scattering in Quantum Dots via Noncommutative Rational Functions.” <i>Annales Henri Poincaré </i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00023-021-01085-6\">https://doi.org/10.1007/s00023-021-01085-6</a>."},"oa":1,"has_accepted_license":"1","status":"public","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","page":"4205–4269","publisher":"Springer Nature","quality_controlled":"1","date_published":"2021-12-01T00:00:00Z","year":"2021","publication_identifier":{"eissn":["1424-0661"],"issn":["1424-0637"]},"publication_status":"published","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Scattering in quantum dots via noncommutative rational functions","ddc":["510"],"file":[{"date_created":"2022-05-12T12:50:27Z","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"8d6bac0e2b0a28539608b0538a8e3b38","file_id":"11365","success":1,"file_name":"2021_AnnHenriPoincare_Erdoes.pdf","date_updated":"2022-05-12T12:50:27Z","file_size":1162454}],"publication":"Annales Henri Poincaré ","abstract":[{"text":"In the customary random matrix model for transport in quantum dots with M internal degrees of freedom coupled to a chaotic environment via 𝑁≪𝑀 channels, the density 𝜌 of transmission eigenvalues is computed from a specific invariant ensemble for which explicit formula for the joint probability density of all eigenvalues is available. We revisit this problem in the large N regime allowing for (i) arbitrary ratio 𝜙:=𝑁/𝑀≤1; and (ii) general distributions for the matrix elements of the Hamiltonian of the quantum dot. In the limit 𝜙→0, we recover the formula for the density 𝜌 that Beenakker (Rev Mod Phys 69:731–808, 1997) has derived for a special matrix ensemble. We also prove that the inverse square root singularity of the density at zero and full transmission in Beenakker’s formula persists for any 𝜙<1 but in the borderline case 𝜙=1 an anomalous 𝜆−2/3 singularity arises at zero. To access this level of generality, we develop the theory of global and local laws on the spectral density of a large class of noncommutative rational expressions in large random matrices with i.i.d. entries.","lang":"eng"}],"doi":"10.1007/s00023-021-01085-6"},{"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2024-03-25T23:30:22Z","article_type":"original","author":[{"full_name":"Vega, Andrea","first_name":"Andrea","last_name":"Vega"},{"full_name":"Fredes, Isabel","first_name":"Isabel","last_name":"Fredes"},{"first_name":"José","last_name":"O’Brien","full_name":"O’Brien, José"},{"full_name":"Shen, Zhouxin","first_name":"Zhouxin","last_name":"Shen"},{"first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","last_name":"Ötvös","full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983"},{"first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","last_name":"Abualia","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"full_name":"Briggs, Steven P.","first_name":"Steven P.","last_name":"Briggs"},{"full_name":"Gutiérrez, Rodrigo A.","first_name":"Rodrigo A.","last_name":"Gutiérrez"}],"date_created":"2021-08-15T22:01:30Z","_id":"9913","acknowledgement":"This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC).","volume":22,"issue":"9","file_date_updated":"2021-10-05T13:36:42Z","scopus_import":"1","citation":{"ieee":"A. Vega <i>et al.</i>, “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” <i>EMBO Reports</i>, vol. 22, no. 9. Wiley, 2021.","ista":"Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 22(9), e51813.","chicago":"Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös, Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” <i>EMBO Reports</i>. Wiley, 2021. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>.","ama":"Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. <i>EMBO Reports</i>. 2021;22(9). doi:<a href=\"https://doi.org/10.15252/embr.202051813\">10.15252/embr.202051813</a>","apa":"Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez, R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. <i>EMBO Reports</i>. Wiley. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>","mla":"Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” <i>EMBO Reports</i>, vol. 22, no. 9, e51813, Wiley, 2021, doi:<a href=\"https://doi.org/10.15252/embr.202051813\">10.15252/embr.202051813</a>.","short":"A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková, S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021)."},"external_id":{"isi":["000681754200001"],"pmid":["34357701 "]},"isi":1,"pmid":1,"department":[{"_id":"EvBe"},{"_id":"GradSch"}],"month":"09","intvolume":"        22","day":"06","date_published":"2021-09-06T00:00:00Z","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"publication_status":"published","year":"2021","quality_controlled":"1","publisher":"Wiley","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10303"}]},"article_number":"e51813","article_processing_charge":"Yes","has_accepted_license":"1","oa":1,"oa_version":"Published Version","status":"public","doi":"10.15252/embr.202051813","publication":"EMBO Reports","abstract":[{"text":"Nitrate commands genome-wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild-type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.","lang":"eng"}],"ddc":["580"],"file":[{"file_size":3144854,"date_updated":"2021-10-05T13:36:42Z","success":1,"file_name":"2021_EmboR_Vega.pdf","file_id":"10090","checksum":"750de03dc3b715c37090126c1548ba13","creator":"cchlebak","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-10-05T13:36:42Z"}],"title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article"},{"citation":{"mla":"Peruzzo, Matilda. <i>Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9920\">10.15479/at:ista:9920</a>.","short":"M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics, Institute of Science and Technology Austria, 2021.","apa":"Peruzzo, M. (2021). <i>Geometric superinductors and their applications in circuit quantum electrodynamics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9920\">https://doi.org/10.15479/at:ista:9920</a>","ista":"Peruzzo M. 2021. Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria.","chicago":"Peruzzo, Matilda. “Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9920\">https://doi.org/10.15479/at:ista:9920</a>.","ama":"Peruzzo M. Geometric superinductors and their applications in circuit quantum electrodynamics. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9920\">10.15479/at:ista:9920</a>","ieee":"M. Peruzzo, “Geometric superinductors and their applications in circuit quantum electrodynamics,” Institute of Science and Technology Austria, 2021."},"day":"19","month":"08","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"author":[{"orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda"}],"keyword":["quantum computing","superinductor","quantum metrology"],"date_updated":"2024-09-10T12:23:56Z","file_date_updated":"2021-09-06T08:39:47Z","_id":"9920","date_created":"2021-08-16T09:44:09Z","abstract":[{"text":"This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented.","lang":"eng"}],"doi":"10.15479/at:ista:9920","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","title":"Geometric superinductors and their applications in circuit quantum electrodynamics","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"ddc":["539"],"file":[{"relation":"source_file","date_created":"2021-08-16T09:33:21Z","content_type":"application/x-zip-compressed","creator":"mperuzzo","access_level":"closed","checksum":"3cd1986efde5121d7581f6fcf9090da8","file_id":"9924","date_updated":"2021-09-06T08:39:47Z","file_name":"GeometricSuperinductorsForCQED.zip","file_size":151387283},{"checksum":"50928c621cdf0775d7a5906b9dc8602c","creator":"mperuzzo","access_level":"open_access","content_type":"application/pdf","relation":"main_file","date_created":"2021-08-18T14:20:06Z","file_size":17596344,"date_updated":"2021-09-06T08:39:47Z","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf","file_id":"9939"},{"date_updated":"2021-09-06T08:39:47Z","description":"Extra copy of the thesis as PDF/A-2b","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf","file_id":"9940","file_size":17592425,"relation":"other","date_created":"2021-08-18T14:20:09Z","checksum":"37f486aa1b622fe44af00d627ec13f6c","access_level":"closed","creator":"mperuzzo","content_type":"application/pdf"}],"publisher":"Institute of Science and Technology Austria","page":"149","publication_identifier":{"isbn":["978-3-99078-013-8"],"issn":["2663-337X"]},"publication_status":"published","year":"2021","date_published":"2021-08-19T00:00:00Z","status":"public","oa_version":"Published Version","oa":1,"has_accepted_license":"1","supervisor":[{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink"}],"article_processing_charge":"No","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"9928","status":"public","relation":"part_of_dissertation"},{"id":"8755","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}]},{"status":"public","oa_version":"Published Version","oa":1,"has_accepted_license":"1","article_processing_charge":"No","ec_funded":1,"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"13057"},{"id":"9920","status":"public","relation":"dissertation_contains"}]},"publisher":"American Physical Society","quality_controlled":"1","page":"040341","year":"2021","publication_identifier":{"eissn":["2691-3399"]},"publication_status":"published","date_published":"2021-11-24T00:00:00Z","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"file":[{"access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","checksum":"36eb41ea43d8ca22b0efab12419e4eb2","relation":"main_file","date_created":"2022-01-18T11:29:33Z","file_size":4247422,"file_id":"10641","date_updated":"2022-01-18T11:29:33Z","success":1,"file_name":"2021_PRXQuantum_Peruzzo.pdf"}],"ddc":["530"],"abstract":[{"lang":"eng","text":"There are two elementary superconducting qubit types that derive directly from the quantum harmonic oscillator. In one, the inductor is replaced by a nonlinear Josephson junction to realize the widely used charge qubits with a compact phase variable and a discrete charge wave function. In the other, the junction is added in parallel, which gives rise to an extended phase variable, continuous wave functions, and a rich energy-level structure due to the loop topology. While the corresponding rf superconducting quantum interference device Hamiltonian was introduced as a quadratic quasi-one-dimensional potential approximation to describe the fluxonium qubit implemented with long Josephson-junction arrays, in this work we implement it directly using a linear superinductor formed by a single uninterrupted aluminum wire. We present a large variety of qubits, all stemming from the same circuit but with drastically different characteristic energy scales. This includes flux and fluxonium qubits but also the recently introduced quasicharge qubit with strongly enhanced zero-point phase fluctuations and a heavily suppressed flux dispersion. The use of a geometric inductor results in high reproducibility of the inductive energy as guaranteed by top-down lithography—a key ingredient for intrinsically protected superconducting qubits."}],"publication":"PRX Quantum","doi":"10.1103/PRXQuantum.2.040341","file_date_updated":"2022-01-18T11:29:33Z","issue":"4","volume":2,"acknowledgement":"We thank W. Hughes for analytic and numerical modeling during the early stages of this work, J. Koch for discussions and support with the scqubits package, R. Sett, P. Zielinski, and L. Drmic for software development, and G. Katsaros for equipment support, as well as the MIBA workshop and the Institute of Science and Technology Austria nanofabrication facility. We thank I. Pop, S. Deleglise, and E. Flurin for discussions. This work was supported by a NOMIS Foundation research grant, the Austrian Science Fund (FWF) through BeyondC (F7105), and IST Austria. M.P. is the recipient of a Pöttinger scholarship at IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.","_id":"9928","date_created":"2021-08-17T08:14:18Z","author":[{"full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","first_name":"Farid","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773"},{"full_name":"Szep, Gregory","first_name":"Gregory","last_name":"Szep"},{"full_name":"Trioni, Andrea","first_name":"Andrea","last_name":"Trioni","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Redchenko, Elena","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko"},{"full_name":"Zemlicka, Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"article_type":"original","keyword":["quantum physics","mesoscale and nanoscale physics"],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-09-07T13:31:22Z","day":"24","intvolume":"         2","arxiv":1,"department":[{"_id":"JoFi"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"month":"11","isi":1,"external_id":{"isi":["000723015100001"],"arxiv":["2106.05882"]},"citation":{"short":"M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, PRX Quantum 2 (2021) 040341.","apa":"Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M., &#38; Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">https://doi.org/10.1103/PRXQuantum.2.040341</a>","mla":"Peruzzo, Matilda, et al. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” <i>PRX Quantum</i>, vol. 2, no. 4, American Physical Society, 2021, p. 040341, doi:<a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">10.1103/PRXQuantum.2.040341</a>.","ista":"Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM. 2021. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. PRX Quantum. 2(4), 040341.","ama":"Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. <i>PRX Quantum</i>. 2021;2(4):040341. doi:<a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">10.1103/PRXQuantum.2.040341</a>","chicago":"Peruzzo, Matilda, Farid Hassani, Gregory Szep, Andrea Trioni, Elena Redchenko, Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” <i>PRX Quantum</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">https://doi.org/10.1103/PRXQuantum.2.040341</a>.","ieee":"M. Peruzzo <i>et al.</i>, “Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction,” <i>PRX Quantum</i>, vol. 2, no. 4. American Physical Society, p. 040341, 2021."},"project":[{"grant_number":"F07105","call_identifier":"FWF","name":"Integrating superconducting quantum circuits","_id":"26927A52-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"2622978C-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1"},{"citation":{"apa":"Czumaj, A., Davies, P., &#38; Parter, M. (2021). Component stability in low-space massively parallel computation. In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i> (pp. 481–491). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3465084.3467903\">https://doi.org/10.1145/3465084.3467903</a>","mla":"Czumaj, Artur, et al. “Component Stability in Low-Space Massively Parallel Computation.” <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2021, pp. 481–491, doi:<a href=\"https://doi.org/10.1145/3465084.3467903\">10.1145/3465084.3467903</a>.","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 481–491.","ista":"Czumaj A, Davies P, Parter M. 2021. Component stability in low-space massively parallel computation. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 481–491.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Component Stability in Low-Space Massively Parallel Computation.” In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, 481–491. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3465084.3467903\">https://doi.org/10.1145/3465084.3467903</a>.","ama":"Czumaj A, Davies P, Parter M. Component stability in low-space massively parallel computation. In: <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2021:481–491. doi:<a href=\"https://doi.org/10.1145/3465084.3467903\">10.1145/3465084.3467903</a>","ieee":"A. Czumaj, P. Davies, and M. Parter, “Component stability in low-space massively parallel computation,” in <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2021, pp. 481–491."},"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"conference":{"end_date":"2021-07-30","location":"Virtual, Italy","start_date":"2021-07-26","name":"PODC: Principles of Distributed Computing"},"external_id":{"isi":["000744439800049"],"arxiv":["2106.01880"]},"isi":1,"department":[{"_id":"DaAl"}],"month":"07","day":"21","arxiv":1,"date_updated":"2023-08-17T07:11:32Z","author":[{"full_name":"Czumaj, Artur","first_name":"Artur","last_name":"Czumaj"},{"full_name":"Davies, Peter","orcid":"0000-0002-5646-9524","id":"11396234-BB50-11E9-B24C-90FCE5697425","last_name":"Davies","first_name":"Peter"},{"full_name":"Parter, Merav","last_name":"Parter","first_name":"Merav"}],"date_created":"2021-08-17T18:11:16Z","_id":"9933","acknowledgement":"This work is partially supported by a Weizmann-UK Making Connections Grant, the Centre for Discrete Mathematics and its Applications (DIMAP), IBM Faculty Award, EPSRC award EP/V01305X/1, European Research Council (ERC) Grant No. 949083, the Minerva foundation with funding from the Federal German Ministry for Education and Research No. 713238, and the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No 754411.","doi":"10.1145/3465084.3467903","abstract":[{"text":"In this paper, we study the power and limitations of component-stable algorithms in the low-space model of Massively Parallel Computation (MPC). Recently Ghaffari, Kuhn and Uitto (FOCS 2019) introduced the class of component-stable low-space MPC algorithms, which are, informally, defined as algorithms for which the outputs reported by the nodes in different connected components are required to be independent. This very natural notion was introduced to capture most (if not all) of the known efficient MPC algorithms to date, and it was the first general class of MPC algorithms for which one can show non-trivial conditional lower bounds. In this paper we enhance the framework of component-stable algorithms and investigate its effect on the complexity of randomized and deterministic low-space MPC. Our key contributions include: 1) We revise and formalize the lifting approach of Ghaffari, Kuhn and Uitto. This requires a very delicate amendment of the notion of component stability, which allows us to fill in gaps in the earlier arguments. 2) We also extend the framework to obtain conditional lower bounds for deterministic algorithms and fine-grained lower bounds that depend on the maximum degree Δ. 3) We demonstrate a collection of natural graph problems for which non-component-stable algorithms break the conditional lower bound obtained for component-stable algorithms. This implies that, for both deterministic and randomized algorithms, component-stable algorithms are conditionally weaker than the non-component-stable ones.\r\n\r\nAltogether our results imply that component-stability might limit the computational power of the low-space MPC model, paving the way for improved upper bounds that escape the conditional lower bound setting of Ghaffari, Kuhn, and Uitto.","lang":"eng"}],"publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","title":"Component stability in low-space massively parallel computation","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"conference","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2106.01880"}],"year":"2021","publication_status":"published","publication_identifier":{"isbn":["9781450385480"]},"date_published":"2021-07-21T00:00:00Z","quality_controlled":"1","publisher":"Association for Computing Machinery","page":"481–491","article_processing_charge":"No","language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Submitted Version","status":"public","oa":1},{"external_id":{"isi":["000744439800048"]},"citation":{"ama":"Czumaj A, Davies P, Parter M. Improved deterministic (Δ+1) coloring in low-space MPC. In: <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2021:469–479. doi:<a href=\"https://doi.org/10.1145/3465084.3467937\">10.1145/3465084.3467937</a>","ista":"Czumaj A, Davies P, Parter M. 2021. Improved deterministic (Δ+1) coloring in low-space MPC. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 469–479.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.” In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, 469–479. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3465084.3467937\">https://doi.org/10.1145/3465084.3467937</a>.","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 469–479.","apa":"Czumaj, A., Davies, P., &#38; Parter, M. (2021). Improved deterministic (Δ+1) coloring in low-space MPC. In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i> (pp. 469–479). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3465084.3467937\">https://doi.org/10.1145/3465084.3467937</a>","mla":"Czumaj, Artur, et al. “Improved Deterministic (Δ+1) Coloring in Low-Space MPC.” <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2021, pp. 469–479, doi:<a href=\"https://doi.org/10.1145/3465084.3467937\">10.1145/3465084.3467937</a>.","ieee":"A. Czumaj, P. Davies, and M. Parter, “Improved deterministic (Δ+1) coloring in low-space MPC,” in <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2021, pp. 469–479."},"conference":{"location":"Virtual, Italy","start_date":"2021-07-26","name":"PODC: Symposium on Principles of Distributed Computing","end_date":"2021-07-30"},"project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"day":"21","month":"07","department":[{"_id":"DaAl"}],"isi":1,"author":[{"first_name":"Artur","last_name":"Czumaj","full_name":"Czumaj, Artur"},{"full_name":"Davies, Peter","orcid":"0000-0002-5646-9524","first_name":"Peter","id":"11396234-BB50-11E9-B24C-90FCE5697425","last_name":"Davies"},{"last_name":"Parter","first_name":"Merav","full_name":"Parter, Merav"}],"date_updated":"2023-08-17T07:11:03Z","acknowledgement":"This work is partially supported by a Weizmann-UK Making Connections Grant, the Centre for Discrete Mathematics and its Applications (DIMAP), IBM Faculty Award, EPSRC award EP/V01305X/1, European Research Council (ERC) Grant No. 949083, the Minerva foundation with funding from the Federal German Ministry for Education and Research No. 713238, and the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No 754411.","_id":"9935","date_created":"2021-08-17T18:14:15Z","abstract":[{"text":"We present a deterministic O(log log log n)-round low-space Massively Parallel Computation (MPC) algorithm for the classical problem of (Δ+1)-coloring on n-vertex graphs. In this model, every machine has sublinear local space of size n^φ for any arbitrary constant φ \\in (0,1). Our algorithm works under the relaxed setting where each machine is allowed to perform exponential local computations, while respecting the n^φ space and bandwidth limitations.\r\n\r\nOur key technical contribution is a novel derandomization of the ingenious (Δ+1)-coloring local algorithm by Chang-Li-Pettie (STOC 2018, SIAM J. Comput. 2020). The Chang-Li-Pettie algorithm runs in T_local =poly(loglog n) rounds, which sets the state-of-the-art randomized round complexity for the problem in the local model. Our derandomization employs a combination of tools, notably pseudorandom generators (PRG) and bounded-independence hash functions.\r\n\r\nThe achieved round complexity of O(logloglog n) rounds matches the bound of log(T_local ), which currently serves an upper bound barrier for all known randomized algorithms for locally-checkable problems in this model. Furthermore, no deterministic sublogarithmic low-space MPC algorithms for the (Δ+1)-coloring problem have been known before.","lang":"eng"}],"publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","doi":"10.1145/3465084.3467937","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"conference","title":"Improved deterministic (Δ+1) coloring in low-space MPC","main_file_link":[{"open_access":"1","url":"http://wrap.warwick.ac.uk/153753"}],"publisher":"Association for Computing Machinery","quality_controlled":"1","page":"469–479","year":"2021","publication_identifier":{"isbn":["978-1-4503-8548-0"]},"publication_status":"published","date_published":"2021-07-21T00:00:00Z","status":"public","oa_version":"Submitted Version","oa":1,"article_processing_charge":"No","ec_funded":1,"language":[{"iso":"eng"}]}]